Ya, Khedira will likely leave as well, he needs playing time and won't be a starter in this team. He and his agent also seem keen to find their way out of Madrid one way or another.
Modric is a very complete midfielder so he won't be a problem. I saw various Bayern matches to check up on Kroos and i did not like that he seemed to lack defensive skills when it comes to positioning, tackling, etc, but he started with the right foot yesterday. I prefer someone more agile and with more speed to be able to cover the flanks so i think i prefer Kroos in the position i outlined in my diagram, rather than in a double pivot or as an Interior. Isco has shown he's capable to play well as an Extremo as shown against Bayern and Barca for example, and yesterday he impressed me with what he did as an Interior/extremo and thus i made a video about it. James will have to learn, he has the physical and technical qualities to be a good interior (he's a bit faster than Isco and that helps), between Isco and James growing, and compact play, i am optimistic.
I really don't think Falcao is going to Madrid. AS have more or less been the ones really milking that, and have looked very agenda driven at that.
Dismantling is not the word i would use to describe this Madrid side, the purchases can be argued plenty but it is of my opinion that the squad is pretty complete as it stands.
Yes, i've seen plenty of sources talking about not having a "midfield destroyer", but team equilibrium and balance is more about player roles, tactics, and working together.
Illarramendi,Alonso,Kroos,Modric,James, and Isco, are more than enough to pull of the 442/433 madrid pulled out against bayern, barca, and atletico for example.